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Papers of Note: Jan 18, 2011


Rapid detection of genetic variants in hypertrophic cardiomyopathy by custom DNA resequencing array in clinical practice.
Fokstuen S, Munoz A, Melacini P, Iliceto S, et al.
J Med Genet. 2011 Jan 14. [Epub ahead of print]

A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing.
Guo L, Liang T, Lu Z.
Biosystems. 2011 Jan 12. [Epub ahead of print]

Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution.
Potapova A, Albat C, Hasemeier B, Hauszler K, et al.
BMC Biotechnol. 2011 Jan 14;11(1):6. [Epub ahead of print]

Resequencing of 29 candidate genes in patients with familial and sporadic amyotrophic lateral sclerosis.
Daoud H, Valdmanis PN, Gros-Louis F, Belzil V, et al.
Arch Neurol. 2011 Jan 10. [Epub ahead of print]

Transpositional landscape of rice genome revealed by paired-end mapping of high-throughput resequencing data.
Sabot F, Picault N, Elbaidouri M, Llauro C, et al.
Plant J. 2011 Jan 10. doi: 10.1111/j.1365-313X.2011.04492.x. [Epub ahead of print]

Robust computational analysis of rRNA hypervariable tag datasets.
Sipos M, Jeraldo P, Chia N, Qu A, et al.
PLoS One. 2010 Dec 31;5(12):e15220.

De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification.
Garg R, Patel RK, Tyagi AK, Jain M.
DNA Res. 2011 Jan 7. [Epub ahead of print]

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Marçais G, Kingsford C.
Bioinformatics. 2011 Jan 7. [Epub ahead of print]

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X-MATE: A flexible system for mapping short read data.
Wood DL, Xu Q, Pearson JV, Cloonan N, Grimmond SM.
Bioinformatics. 2011 Jan 6. [Epub ahead of print]

Detecting structural variations in the human genome using next generation sequencing.
Xi R, Kim TM, Park PJ.
Brief Funct Genomics. 2011 Jan 6. [Epub ahead of print]

Massive genomic rearrangement acquired in a single catastrophic event during cancer development.
Stephens PJ, Greenman CD, Fu B, Yang F, et al.
Cell. 2011 Jan 7;144(1):27-40.

The complete genomic sequence of HLA-DRB1*10:01:01 was identified by sequencing in a Han Chinese individual.
Liu B, Xiong Y, Tian C, Zhong Y, Liu SM.
Tissue Antigens. 2011 Feb;77(2):159-60. doi: 10.1111/j.1399-0039.2010.01593.x.

Quantification of gene transcripts with deep sequencing analysis of gene expression (DSAGE) using 1 to 2 µg total RNA.
C Christodoulou D, Gorham JM, Kawana M, Depalma SR, et al.
Curr Protoc Mol Biol. 2011 Jan;Chapter 25:Unit25B.9.

Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study.
Chiu RW, Akolekar R, Zheng YW, Leung TY, et al.
BMJ. 2011 Jan 11;342:c7401. doi: 10.1136/bmj.c7401.

Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments.
McIver LJ, Fondon JW 3rd, Skinner MA, Garner HR.
Genomics. 2011 Jan 8. [Epub ahead of print]

Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes.
Rincon-Restrepo M, Mikhailova E, Bayley H, Maglia G.
Nano Lett. 2011 Jan 11. [Epub ahead of print]

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Carrier testing for severe childhood recessive diseases by next-generation sequencing.
Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, et al.
Sci Transl Med. 2011 Jan 12;3(65):65ra4.

Improved nucleotide selectivity and termination of 3'-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates.
Litosh VA, Wu W, Stupi BP, Wang J, et al.
Nucleic Acids Res. 2011 Jan 11. [Epub ahead of print]

Shape-based peak identification for ChIP-seq.
Hower V, Evans SN, Pachter L.
BMC Bioinformatics. 2011 Jan 12;12(1):15.

Multiplexed shotgun genotyping for rapid and efficient genetic mapping.
Andolfatto P, Davison D, Erezyilmaz D, Hu TT, et al.
Genome Res. 2011 Jan 13. [Epub ahead of print]

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.
Hao X, Jiang R, Chen T.
Bioinformatics. 2011 Jan 13. [Epub ahead of print]

A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
Bioinformatics. 2011 Jan 13. [Epub ahead of print]

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Xu G, Deng N, Zhao Z, Judeh T, et al.
Source Code Biol Med. 2011 Jan 13;6(1):2. [Epub ahead of print]

Combining gene prediction methods to improve metagenomic gene annotation.
Yok NG, Rosen GL.
BMC Bioinformatics. 2011 Jan 13;12(1):20.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.